How to plan an MRCP protocol

This step-by-step guide is for MRI students, radiographers, and technologists who wish to improve their planning skills and master the MRCP protocol.

What you will learn:

1. Key factors in MRCP, including trade-offs.
2. Patient and scanner setup tips.
3. Best pulse sequences and planning techniques.
4. Ways to avoid common artifacts.
5. What great MRCP images should look like.

MRCP, or magnetic resonance cholangiopancreatography, evaluates the biliary and pancreatic duct systems using heavily T2-weighted imaging. This makes static fluids like bile and pancreatic juice appear bright, without invasive procedures or ionizing radiation. Stones contain no free fluid, so they appear as dark filling defects against that bright background.

The protocol combines routine upper-abdominal sequences with dedicated MRCP acquisitions, so we assess both the abdominal organs and the fine duct anatomy in one study.

MRCP is now the standard non-invasive test for suspected common bile duct stones and biliary obstruction, with reported sensitivity generally in the 85–100% range and specificity around 90–100%. ERCP is increasingly reserved for cases that need therapy rather than diagnosis.

How to Balance the 3 Trade-offs in MRCP

In MRI, we always face a trade-off between 3 key metrics:

1. Scan Time: How fast a pulse sequence can be completed.
2. Resolution: How much detail the image can display.
3. SNR: How clear the image is, how much signal relative to noise.

Improving one of these metrics reduces the performance of the others. To decide what trade-offs to make, we must consider the needs of each clinical situation.

For MRCP, we face three specific challenges:

• Tiny structures. The main pancreatic duct is usually only a few millimeters wide, up to about 3 mm on MRCP depending on location and age, and stones or strictures can be smaller still. Without high spatial resolution, partial volume averaging blurs them together and small findings vanish.
• Fluid-based contrast. The duct signal comes mainly from fluid. Heavily T2-weighted imaging keeps static bile and pancreatic juice bright against a darker background, so we need enough SNR to hold the bright-fluid to dark-stone distinction clear. That gets SNR-sensitive when voxels are small and echo times are long.
• Constant motion. The upper abdomen moves with breathing and bowel motion, and the high-detail scan takes minutes.

Therefore, we typically:

1. Prioritize resolution because the fine duct detail is the diagnosis, and
2. Keep SNR high enough for clarity.

But neither matters until motion is controlled, and one scan usually cannot maximize resolution, SNR, and speed at once.

So the protocol takes a two-pronged approach, splitting its sequences into two groups: one optimized for detail, one for speed.

1. The respiratory-triggered sequence group: 1) resolution, 2) SNR, 3) scan time

These sequences acquire data during a consistent part of the breathing cycle, usually near end-expiration, which reduces motion rather than freezing it, at the cost of minutes. Having already spent the time, they keep resolution and SNR high, so scan time comes last.

The 3D MRCP is the most important sequence. Its thin near-isotropic voxels, roughly 1.4 mm in-plane by 1.6 mm slice, resolve small stones and fine ducts and reconstruct in any plane, and its volumetric readout supplies the SNR those thin slices spend. The coronal and fat-suppressed T2 images ride along in the same group, trading time for clean, detailed anatomy.

2. The breath-hold sequence group: 1) scan time, 2) SNR, 3) resolution

These sequences finish inside a single breath-hold or a single shot, so respiratory motion has little chance to blur them, though bowel motion or a failed breath-hold still can.

Speed comes first, and detail is what gets sacrificed. The thick slab collapses through-plane detail into one projection, and single-shot readouts come out softer than the triggered images. This group keeps the study diagnostic when the patient cannot hold still or breathe regularly.

Strategy and Priority for Each MRCP Sequence

This table shows a breakdown of every sequence in standard MRCP protocol, the motion-control strategy we use, and what to prioritize in acquisition.

Note on Other MRCP Variants

Grouping and triggering differ by vendor and site, so a sequence that is respiratory-triggered here may be run breath-hold elsewhere.

Some centers use breath-hold 3D MRCP with compressed sensing to bring near-3D duct detail into one breath-hold, though heavy acceleration can reduce small-duct visibility.

Secretin MRCP changes the trade-off further, adding repeated timed thick-slab images after IV secretin to assess pancreatic duct filling and function, where temporal timing outranks spatial resolution. These are not the sequences demonstrated in this video.

MRCP Health Conditions and the MRI Sequences That Reveal Them

The MRCP study can help us diagnose a wide range of health conditions. The table below lists some of the most common conditions and what pulse sequences reveal them:

The step-by-step guide below will show you how to set up and perform an MRCP protocol in practice.

We will perform the protocol in 3 parts:

1. Set up the Patient and MRI Scanner
2. Plan and Acquire the Protocol Sequences
3. Review the Images

Part 1: Set up the Patient and MRI Scanner

1. Prepare the Patient

MRCP is one of the few protocols where preparation before the patient reaches the table directly affects image quality.

• Fasting: Ask the patient to fast for 4–6 hours when the clinical situation allows. This reduces bright fluid in the stomach and duodenum, and lets the gallbladder distend.
• Negative oral contrast (optional, site-dependent): Bright gastric and duodenal fluid can sit on top of the common bile duct and hide it. Commercial ferumoxsil agents are purpose-built for this. Many departments use pineapple juice instead, which works because its naturally high manganese content shortens the T2 of the fluid it mixes with, so at MRCP’s very long echo times that fluid loses nearly all signal. Published protocols typically give 200–400 mL, 10–30 minutes before scanning. Always follow your own institution’s policy.
• Breathing coaching: Practice breath-hold instructions before the patient enters the bore, and test both exhale and inhale. Many patients hold their breath far more reliably one way, and picking the better one keeps slice positions consistent between sequences.

2. Position the Patient in the Scanner

Lay the patient supine with the upper abdomen centered at the scanner’s isocenter.

Use an anterior body array coil on top of the upper abdomen, combined with the posterior spine coil integrated into the scanner table. This gives full signal coverage of the liver, gallbladder, biliary tree, and pancreas.

Arms can be positioned above the head or alongside the body. If they rest alongside the body they sit near the field of view in the right-to-left direction, which is why fold-over suppression matters on the coronal sequences.

✅ Correct Patient Positioning:

3. Check the Scanner’s Hardware Settings

Once the patient is in place, review your scanner’s hardware settings.

In this guide, we will use the following settings:

Scanner Setting	Value	Why This Value
Magnetic field strength	1.5 T	Enables high Signal-to-Noise Ratio, which gives superior image quality. 1.5 T is also less prone to susceptibility and dielectric artifacts in the abdomen than 3 T.
Maximum gradient strength	45 mT/m	Enables faster acquisitions while preserving high image quality.
Receive coil	Anterior body array + posterior spine coil	Full anterior-to-posterior coverage of the upper abdomen with strong signal reception.

This hardware setup is widely used in clinical practice. It balances acquisition time, image quality, and patient comfort.

4. Capture the Initial Localizer Images

Before we can perform any MRI protocol, we must always capture initial localizer images of the patient. These images act as a guide for planning the detailed scans we will perform next.

Select the abdominal region, save it, and run the localizers.

We should always capture localizers in three planes:

1. Axial
2. Sagittal
3. Coronal

Once acquired, drag and drop the localizer images into the three viewports. Then scroll through each stack to locate a central slice that clearly shows the anatomy of the upper abdomen.

✅ Correct Setup of Localizer Images for MRCP:

Part 2: Plan and Acquire the Protocol Sequences

When all preparations are ready, we can start planning and acquiring the protocol sequences.

Let’s go through the pulse sequences a standard MRCP protocol includes, why we perform them, and how to set them up.

The 6 Sequences of a Standard MRCP Protocol

1. Coronal T2 TSE
2. Axial T2 FS TSE
3. Axial T2 SS-TSE
4. Axial GRE Dixon
5. 3D MRCP
6. Radial SS-TSE FS

Sequences 1, 2, and 5 belong to the respiratory-triggered group. Sequences 3, 4, and 6 belong to the breath-hold group.

Note! Your facility may have its own local policies, so the protocol might differ in some of these sequences. If they differ, then always follow your own institution's guidelines.

In the sections below, we go through how to plan and set up each sequence.

1. Planning Coronal T2 TSE

✅ Correct Planning:

Planning Instructions:

• Plan in the true coronal plane, covering the entire hepatobiliary system.
• Use appropriate geometry parameters:
  • Coverage: From the anterior abdominal wall back to the kidneys, including liver, gallbladder, pancreas, spleen, and upper kidneys.
  • Slice number: 32–38, enough for that anterior-to-posterior block.
  • Slice thickness: 6 mm, standard overview thickness.
  • Slice gap: 1 mm, prevents crosstalk while maintaining continuity.
• Set the fold-over direction (phase encoding) to right-to-left (RL) and activate fold-over suppression, so the arms and body wall do not alias into the image.
• Acquire with respiratory triggering. This is a multi-shot TSE that takes a few minutes, so it follows the breathing cycle rather than a breath-hold.

Tip: You can display your slices in either box view or slice view. Pick whichever helps you check coverage, angle, and position most clearly.

Parameters for Coronal T2 TSE:

Parameter	Recommended Values	Why These Values
Effective Echo Time (TE)	80–100 ms	Long TE is required for T2 contrast.
Repetition Time (TR)	2,000–2,500 ms	Long TR is required for T2 contrast. With respiratory triggering, the effective TR follows the breathing cycle.
Field-of-View (FOV)	380 × 380 mm	Covers the full width of the upper abdomen at this patient size.
Matrix	320 × 224	High read matrix for in-plane detail, reduced phase matrix to hold scan time down on a multi-shot readout.
Foldover Direction (Phase)	Right-to-Left (RL)	Matches the shape of the coronal upper abdomen.
Number of Slices	32–38	Enough to cover from the anterior abdominal wall back to the kidneys.
Slice Thickness	6 mm	Standard overview thickness, keeps SNR high without excessive scan time.
Slice Gap	1 mm	Prevents crosstalk between slices while maintaining continuity.
NEX / Averages	1	Keep as low as possible to hold scan time reasonable on a triggered acquisition.
Bandwidth	220–250 Hz/px	Just above the point where fat-water shift equals one pixel at 1.5 T. Going lower would gain SNR but widen chemical shift at the organ borders.
Turbo Factor / ETL	15–25	A high turbo factor collects many echoes per shot, which is what keeps a multi-shot readout of 35 slices down to a few minutes.
Fold-over Suppression	Yes	Prevents aliasing from the arms and body wall in the RL direction.
Breath-hold Mode	Free breathing	Multi-shot TSE takes minutes, which is far too long for a breath-hold, so it follows the respiratory cycle instead.

2. Planning Axial T2 FS TSE

✅ Correct Planning:

Planning Instructions:

• Plan in the axial plane. Right-click on the axial localizer and set the in-plane position, which also sets the correct orientation under the Geometry tab.
• Use appropriate geometry parameters:
  • Coverage: From the hepatic dome down to the kidneys.
  • Slice number: 32–38.
  • Slice thickness: 6 mm, with a 1 mm gap.
• Review your slice package on top of a high-resolution image, such as the coronal T2, and scroll through to confirm the abdominal dome and kidneys are both covered.
• Set the fold-over direction (phase encoding) to anterior-to-posterior (AP) to prevent aliasing.
• Fold-over suppression can stay off here, since no anatomy extends beyond the field of view in the AP direction. Leaving it off also reduces scan time.
• Acquire with respiratory triggering, the same as the coronal T2.

Parameters for Axial T2 FS TSE:

Parameter	Recommended Values	Why These Values
Effective Echo Time (TE)	80–95 ms	Long TE is required for T2 contrast.
Repetition Time (TR)	2,000–2,500 ms	Long TR is required for T2 contrast and allows enough slices per acquisition.
Field-of-View (FOV)	380 × 380 mm	Sized to the patient's abdominal width, matching the coronal T2.
Matrix	320 × 256	Higher phase matrix than the coronal T2, resolving wall thickening and small fluid collections.
Foldover Direction (Phase)	Anterior-to-Posterior (AP)	Matches the shape of the axial abdomen and prevents wraparound.
Number of Slices	32–38	Enough to cover from the hepatic dome to the kidneys.
Slice Thickness	6 mm	Standard thickness for an axial abdominal survey.
Slice Gap	1 mm	Prevents crosstalk while maintaining continuity.
NEX / Averages	2	Higher than the coronal T2, since the fat suppression pulse removes signal that has to be recovered.
Bandwidth	220–250 Hz/px	Kept low to protect the SNR that the fat suppression pulse removes, while staying high enough to hold chemical shift to about one pixel at 1.5 T.
Turbo Factor / ETL	18	Matched to the 80 ms effective echo time to keep acquisition time suitable.
Fold-over Suppression	No	No anatomy extends beyond the FOV in the AP direction, and leaving it off shortens scan time.
Fat Suppression	Spectral	Removes fat signal so inflammation and edema stand out against a darker background.
Breath-hold Mode	Free breathing	Multi-shot TSE needs minutes to acquire, so it follows the respiratory cycle instead of a breath-hold.

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Parameter	Recommended Values	Why These Values
Effective Echo Time (TE)	120–140 ms	Higher TE than the axial T2 FS gives better fluid-to-soft-tissue contrast, leaning toward highlighting fluid-containing structures.
Repetition Time (TR)	1,000–1,500 ms	Each slice is a single shot, so TR sets the interval between slices rather than the contrast.
Field-of-View (FOV)	380 × 380 mm	Copied from the axial T2 FS for direct comparison.
Matrix	320 × 256	Copied from the axial T2 FS. The softer look comes from the single-shot readout and half-Fourier filling, not from a smaller matrix.
Foldover Direction (Phase)	Anterior-to-Posterior (AP)	Matches the axial anatomy shape.
Number of Slices	32–38	Copied from the axial T2 FS.
Slice Thickness	6 mm	Copied from the axial T2 FS.
Slice Gap	1 mm	Copied from the axial T2 FS.
NEX / Averages	1	Single average, since the point of this sequence is speed.
Bandwidth	600–700 Hz/px	Roughly three times the 1.5 T minimum. Wide bandwidth shortens the readout and echo spacing, which is what lets a whole slice be read in one shot.
Partial Fourier	Phase-conjugate (half-Fourier)	Fills only part of k-space and reconstructs the rest, which is what enables the single-shot readout.
Fold-over Suppression	No	Copied from the axial T2 FS, keeps acquisition fast.
Breath-hold Mode	Exhale or inhale	Each slice freezes in roughly one second, so the stack fits inside one or two breath-holds. Pick whichever your patient holds more reliably.

4. Planning Axial GRE Dixon

✅ Correct Planning:

Planning Instructions:

• Copy the slice geometry from one of your previous axial sequences using the Custom copy option.
• This time, remove the matrix sizes from the copy while keeping everything else. The Dixon runs at slightly lower in-plane resolution because it is acquired in a breath-hold.
• Through-plane resolution and central position stay the same, so the radiologist can compare all sequences at matching levels.
• Acquire as a breath-hold.

Planning for Axial GRE Dixon:

Parameter	Recommended Values	Why These Values
Echo Time (TE)	4.5 ms	At 1.5 T, fat and water return to the in-phase condition every 2.24 ms, so 4.5 ms lands on an in-phase echo.
Second-echo Time Difference	2.24 ms	Half a fat-water phase cycle at 1.5 T, placing the second echo at 6.74 ms, which is opposed-phase. The two echoes are what make the Dixon separation possible.
Repetition Time (TR)	150–200 ms	Short TR for a fast T1-weighted gradient echo readout.
Flip Angle	15°	Low flip angle suited to the short TR.
Field-of-View (FOV)	380 × 380 mm	Copied from the axial T2 sequences.
Matrix	320 × 224	Reduced phase matrix compared with the axial T2 sequences, which is the resolution cost of fitting the acquisition into one breath-hold.
Foldover Direction (Phase)	Anterior-to-Posterior (AP)	Matches the axial anatomy shape.
Number of Slices	32–38	Copied from the axial T2 sequences.
Slice Thickness	6 mm	Keeps through-plane resolution equivalent to the other axials.
Slice Gap	1 mm	Copied from the axial T2 sequences.
NEX / Averages	1	Single average keeps scan time short enough for one breath-hold.
Bandwidth	600–700 Hz/px	Wide bandwidth is what allows both echoes to be read at the exact timings the Dixon method needs, and it keeps chemical shift well under a pixel.
Fold-over Suppression	No	No anatomy extends beyond the FOV in the AP direction.
Fat Suppression	None (reconstructed)	Fat and water are separated mathematically from the two echoes, not by a suppression pulse.
Breath-hold Mode	Exhale or inhale	Fast gradient echo readout completes inside a single breath-hold. Match the direction used on the single-shot to keep slice positions consistent.

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